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Zinc in PDB 3nq5: Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant

Enzymatic activity of Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant

All present enzymatic activity of Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant:
1.14.18.1;

Protein crystallography data

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant, PDB code: 3nq5 was solved by M.Sendovski, M.Kanteev, N.Adir, A.Fishman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.93 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.130, 80.850, 147.110, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 30.4

Other elements in 3nq5:

The structure of Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant (pdb code 3nq5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant, PDB code: 3nq5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 3nq5

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Zinc binding site 1 out of 10 in the Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:28.2
occ:1.00
 OD2 A:ASP287 2.0 24.9 1.0
ND1 A:HIS13 2.0 23.4 1.0
O A:HOH382 2.1 6.4 1.0
O A:HOH324 2.3 17.3 1.0
CG A:ASP287 2.9 25.3 1.0
CE1 A:HIS13 2.9 23.7 1.0
CG A:HIS13 3.1 19.2 1.0
CB A:ASP287 3.4 23.3 1.0
CB A:HIS13 3.6 18.2 1.0
OD1 A:ASP287 3.8 27.4 1.0
NE2 A:HIS13 4.1 24.7 1.0
CD2 A:HIS13 4.2 21.6 1.0
N A:ASN10 4.5 23.9 1.0
CB A:ASN10 4.8 19.3 1.0
CA A:LYS9 4.8 20.8 1.0
CB A:LYS9 4.8 20.4 1.0
CG A:LYS9 4.8 21.1 1.0
CA A:ASP287 4.9 26.5 1.0
OH A:TYR91 4.9 26.0 1.0

Zinc binding site 2 out of 10 in 3nq5

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Zinc binding site 2 out of 10 in the Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:50.5
occ:0.86
 OD1 A:ASP16 2.0 45.8 1.0
O A:HOH400 2.5 26.4 1.0
CG A:ASP16 2.8 43.1 1.0
OD2 A:ASP16 3.1 39.1 1.0
O A:HOH404 3.6 26.4 1.0
CB A:ASP16 4.2 34.1 1.0
O A:HOH314 4.5 10.2 1.0

Zinc binding site 3 out of 10 in 3nq5

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Zinc binding site 3 out of 10 in the Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:59.6
occ:0.86
 NE2 A:HIS49 2.0 16.2 1.0
O B:HOH396 2.2 41.3 1.0
CE1 A:HIS49 2.7 19.6 1.0
CD2 A:HIS49 3.3 19.9 1.0
O A:HOH412 3.4 26.4 1.0
OD1 B:ASN144 3.7 35.4 1.0
ND2 B:ASN144 3.9 33.9 1.0
ND1 A:HIS49 3.9 15.6 1.0
O B:GLN142 3.9 50.9 1.0
CG B:ASN144 4.2 36.1 1.0
CG A:HIS49 4.2 22.1 1.0
O A:HOH320 4.5 24.8 1.0
O A:GLY46 4.6 37.2 1.0

Zinc binding site 4 out of 10 in 3nq5

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Zinc binding site 4 out of 10 in the Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:82.1
occ:1.00
 O A:HOH385 2.7 15.2 1.0
OE2 A:GLU71 2.9 29.8 1.0
O A:HOH398 3.1 26.4 1.0
OE1 A:GLU71 3.2 25.0 1.0
NH1 A:ARG78 3.4 27.5 1.0
CD A:GLU71 3.4 26.4 1.0
CD2 A:LEU74 4.2 25.3 1.0
NH2 A:ARG75 4.4 36.4 1.0
CZ A:ARG78 4.4 23.6 1.0
NH2 A:ARG78 4.5 21.3 1.0
OG1 A:THR271 4.6 18.7 1.0
CG2 A:THR271 4.7 25.9 1.0
CG A:LEU74 4.8 20.4 1.0
CG A:GLU71 4.9 23.9 1.0
CG A:ARG75 5.0 34.0 1.0
CZ A:ARG75 5.0 31.6 1.0

Zinc binding site 5 out of 10 in 3nq5

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Zinc binding site 5 out of 10 in the Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:46.8
occ:0.80
 OD1 A:ASP123 2.1 71.5 1.0
CG A:ASP123 3.2 71.2 1.0
OD2 A:ASP123 3.6 69.2 1.0
CB A:ASP123 4.4 68.1 1.0
O A:ASP123 4.5 78.9 1.0
CA A:ASP123 4.6 66.7 1.0
CD1 A:PHE124 4.8 35.8 1.0
C A:ASP123 4.9 71.7 1.0

Zinc binding site 6 out of 10 in 3nq5

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Zinc binding site 6 out of 10 in the Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:47.7
occ:1.00
 NH1 A:ARG280 1.9 33.0 1.0
NE2 A:HIS279 2.1 23.6 1.0
O A:HOH326 2.3 14.4 1.0
O A:HOH329 2.4 31.8 1.0
CE1 A:HIS279 2.7 20.5 1.0
CZ A:ARG280 3.1 40.4 1.0
CD2 A:HIS279 3.3 23.5 1.0
CD1 A:ILE243 3.5 36.9 1.0
NH2 A:ARG280 3.6 38.2 1.0
ND1 A:HIS279 3.9 27.4 1.0
NE A:ARG280 4.2 44.6 1.0
CG A:HIS279 4.3 24.8 1.0
CG1 A:ILE243 4.3 38.6 1.0
CB A:ALA239 4.3 16.4 1.0
O A:ALA239 4.4 19.6 1.0
CD A:ARG280 4.5 44.5 1.0
C A:ALA239 4.9 19.7 1.0

Zinc binding site 7 out of 10 in 3nq5

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Zinc binding site 7 out of 10 in the Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:23.6
occ:1.00
 OD2 B:ASP287 1.5 25.4 1.0
ND1 B:HIS13 2.0 13.0 1.0
O B:HOH402 2.1 14.3 1.0
CG B:ASP287 2.3 24.7 1.0
O B:HOH404 2.8 12.5 1.0
OD1 B:ASP287 2.8 31.6 1.0
CE1 B:HIS13 2.9 12.3 1.0
CG B:HIS13 3.0 10.9 1.0
CB B:HIS13 3.4 9.6 1.0
CB B:ASP287 3.5 26.1 1.0
NE2 B:HIS13 4.0 11.2 1.0
CD2 B:HIS13 4.1 11.3 1.0
CB B:LYS9 4.2 18.8 1.0
N B:ASN10 4.2 16.9 1.0
CG B:LYS9 4.4 20.5 1.0
CA B:LYS9 4.5 20.2 1.0
CB B:ASN10 4.7 14.3 1.0
CA B:ASP287 4.7 31.6 1.0
CD B:LYS9 4.9 20.8 1.0
CA B:HIS13 4.9 11.6 1.0
C B:LYS9 4.9 16.4 1.0

Zinc binding site 8 out of 10 in 3nq5

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Zinc binding site 8 out of 10 in the Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:61.6
occ:1.00
 OE2 B:GLU71 2.0 27.1 1.0
O B:HOH401 3.0 23.2 1.0
CD B:GLU71 3.0 26.8 1.0
O B:HOH405 3.3 29.5 1.0
NH2 B:ARG75 3.5 20.6 1.0
OE1 B:GLU71 3.5 31.1 1.0
OG1 B:THR271 3.6 27.4 1.0
NH1 B:ARG78 4.0 23.6 1.0
CG B:GLU71 4.2 20.4 1.0
CZ B:ARG75 4.5 22.0 1.0
CG B:ARG75 4.5 21.4 1.0
CD B:ARG75 4.8 21.6 1.0
NE B:ARG75 5.0 26.7 1.0

Zinc binding site 9 out of 10 in 3nq5

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Zinc binding site 9 out of 10 in the Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn505

b:54.2
occ:1.00
 OE2 B:GLU95 1.9 30.0 1.0
O B:HOH310 2.0 22.8 1.0
O B:HOH305 2.1 25.1 1.0
CD B:GLU95 3.0 31.0 1.0
OE1 B:GLU95 3.7 23.5 1.0
O B:HOH383 3.8 39.3 1.0
CG B:GLU95 3.9 25.2 1.0
OE2 B:GLU93 4.1 28.0 1.0
CG1 B:VAL168 4.1 29.1 1.0
NH1 B:ARG236 4.2 26.2 1.0
NH2 B:ARG236 4.4 16.9 1.0
O B:HOH424 4.5 26.4 1.0
CD B:GLU93 4.8 24.2 1.0
CB B:VAL168 4.8 26.4 1.0
CG B:ARG165 4.8 47.9 1.0
CZ B:ARG236 4.8 21.1 1.0
CD1 B:ILE237 4.9 14.5 1.0

Zinc binding site 10 out of 10 in 3nq5

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Zinc binding site 10 out of 10 in the Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Tyrosinase From Bacillus Megaterium R209H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn506

b:36.9
occ:1.00
 O B:HOH332 2.0 15.7 1.0
NE2 B:HIS279 2.0 14.4 1.0
O B:HOH333 2.3 15.1 1.0
CE1 B:HIS279 2.9 18.5 1.0
CD2 B:HIS279 3.1 12.9 1.0
ND1 B:HIS279 4.1 21.3 1.0
O B:ALA239 4.1 20.7 1.0
CG B:HIS279 4.2 18.7 1.0
CD1 B:ILE243 4.3 32.9 1.0
CB B:ALA239 4.4 13.5 1.0
C B:ALA239 4.5 19.6 1.0
CG1 B:ILE243 4.6 34.4 1.0
CA B:ALA239 4.8 14.4 1.0
O B:HOH309 4.9 10.2 1.0

Reference:

M.Sendovski, M.Kanteev, V.Shuster Ben-Yosef, N.Adir, A.Fishman. First Structures of An Active Bacterial Tyrosinase Reveal Copper Plasticity. J.Mol.Biol. V. 405 227 2011.
ISSN: ISSN 0022-2836
PubMed: 21040728
DOI: 10.1016/J.JMB.2010.10.048
Page generated: Wed Aug 20 12:23:24 2025

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